A5026539556- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Ubiquitin and proteasome pathways
- Fungal and yeast genetics research
- Epigenetics and DNA Methylation
- Biofuel production and bioconversion
- Plant Molecular Biology Research
- Diet and metabolism studies
- Nutrition, Genetics, and Disease
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Bioinformatics, and Biomedical Research
- Genetic factors in colorectal cancer
- DNA and Nucleic Acid Chemistry
- Polyamine Metabolism and Applications
- Protein Degradation and Inhibitors
- Cancer-related Molecular Pathways
- CRISPR and Genetic Engineering
- Wireless Communication Networks Research
- Data Stream Mining Techniques
- Stock Market Forecasting Methods
- Plant tissue culture and regeneration
- Enzyme Catalysis and Immobilization
- RNA modifications and cancer
Karolinska Institutet
2013-2022
University of Mumbai
2019
Indian Institute of Technology Bombay
2011-2014
Science for Life Laboratory
2013
Positives and negatives of methylated CpG When the DNA bases cytosine guanine are next to each other, a methyl group is generally added pyrimidine, generating mCpG dinucleotide. This modification alters structure but can also affect function by inhibiting transcription factor (TF) binding. Yin et al. systematically analyzed effect methylation on binding 542 human TFs (see Perspective Hughes Lambert). In addition some TFs, they found that mCpGs promote others, particularly involved in...
Abstract DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured transcriptional activity sequences represent an ~100 times larger space than human genome using massively parallel reporter assays (MPRAs). Machine learning models revealed transcription factors (TFs) generally act in additive manner with weak grammar most enhancers increase from a promoter by mechanism does not appear to involve...
The gene desert upstream of the MYC oncogene on chromosome 8q24 contains susceptibility loci for several major forms human cancer. region shows high conservation between and mouse multiple enhancers that are activated in tumor cells. However, role this normal development has not been addressed. Here we show a 538 kb deletion entire super-enhancer mice results 50% to 80% decrease Myc expression tissues. viable no overt phenotype. they resistant tumorigenesis, most cells isolated from them...
Abstract The mammalian cell cycle is controlled by the E2F family of transcription factors. Typical E2Fs bind to DNA as heterodimers with related dimerization partner (DP) proteins, whereas atypical E2Fs, E2F7 and E2F8 contain two DNA-binding domains (DBDs) act repressors. To understand mechanism repression, we have resolved structure in complex at atomic resolution. We find that first second DBDs resemble typical DP respectively. Using molecular dynamics simulations, biochemical affinity...
Article27 January 2021Open Access Source DataTransparent process Transcriptionally active enhancers in human cancer cells Katja Lidschreiber orcid.org/0000-0001-6319-1076 Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, SwedenThese authors contributed equally to this work Search more papers by author Lisa A Jung orcid.org/0000-0003-4149-1662 Sweden Cell Biomedicum, Solna,...
Point mutations in cancer have been extensively studied but chromosomal gains and losses more challenging to interpret due their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape 1699 colorectal cancers, 256 of which whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout activation screens identified total 79 within peaks regulating cell growth. Genetic functional...
Transcription factor (TF) binding can be studied accurately in vivo with ChIP-exo and ChIP-Nexus experiments. Only fraction of TF mechanisms are yet fully understood accurate knowledge locations patterns TFs is key to understanding that not explained by simple positional weight matrix models. ChIP-exo/Nexus experiments also offer insight on the effect single nucleotide polymorphism (SNP) at sites expression target genes. This an important mechanism action for disease-causing SNPs non-coding...
A stock market is the aggregation of buyers and sellers stocks (shares), which represent ownership claims on businesses may include securities listed a public exchange as well those traded privately. We have seen through years that people incurred high losses led to devastations lives hence need for prediction system arises can be trusted consistent throughout life cycle. Also predicting prices an important task financial time series forecasting, primary interest investors, traders applied...
Abstract DNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. To obtain a global unbiased view relative importance different in expression, we measured transcriptional activity sequences aggregate ∼100 times longer than human genome three cell types. We show enhancers can be classified to main types: classical 1 , closed chromatin chromatin-dependent enhancers, which act via mechanisms differ motif content....
Abstract The gene desert upstream of the Myc oncogene on chromosome 8q24 contains susceptibility loci for several major forms human cancer, including cancers breast, prostate, and colon. region shows high conservation between mouse multiple MYC enhancers that are activated in tumor cells. However, role this normal development has not been addressed. Here we show a 538 kb deletion entire super-enhancer mice results 50 to 80% decrease expression tissues. viable no overt phenotype. they...